Output¶
Using the Output tab you can save your work as tiff, h5, or zarr.
Labels can be exported as mesh files (glb, obj or ply).
Use glb if possible, the other formats are missing the color information,
or merge all segments into a single mesh.
Once you have exported an image, you can create a workflow file to repeat the processing steps you have performed on image batches.
Time Series¶
Time series in Tiff format are exported as OME-TIFF files,
with the TimeIncrement metadata written
when the time spacing is known. Per the OME-TIFF naming convention,
these files carry the .ome.tiff extension.
H5 and zarr exports carry the layout
(axis_order attribute) and the spacing when it is known, so a re-import
recovers the time series and its spacing.
For a 3D time series segmentation, the mesh export writes one file per
timepoint, named {name}_t000.{ext}, {name}_t001.{ext}, and so on, with a
zero-based index. Empty timepoints get their (empty) mesh file too, so the file count
always matches the timepoint count.
Widget: Output¶
- Layer to export: Select all layer to be exported, and (optional) set a custom file name suffix that will be appended at end of the layer name.
- Export directory: Select the directory where the files will be exported
- Number of channels: Add additional layers to the output image
- Export name pattern: Pattern for the exported file name. Use {image_name} to include the layer name, or {file_name} to include the original file name.
- Export format: Export format, if tiff is selected, each layer will be exported as a separate file. If h5 is selected, all layers will be exported in a single file.
- Key: Key to be used in the h5 or zarr file.
- Export Mesh: Convert segmentation to mesh. glb is encuraged, other formats might have missing color, or merge meshes.
- Close mesh: Whether to close the mesh at the edges of the image.
- Rescale to original resolution: Rescale the image to the original voxel size.
- Data Type: Export datatype (uint16 for segmentation) and all others for images.